<tool id="chewbbaca_schemaevaluator" name="chewBBACA SchemaEvaluator" version="@TOOL_VERSION@+galaxy0">
    <description>BSR-Based Allele Calling Algorithm</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        chewBBACA.py SchemaEvaluator
          --cpu \${GALAXY_SLOTS:-1}
          -i '${schema}'
          -t '${threshold}'
        ]]>
    </command>
    <inputs>
        
    </inputs>

    <!-- define outputs -->
    <outputs>
        <data format="tabular" name="statistics" label="${tool.name}: on ${on_string}: Statistics" />
        <data format="tabular" name="contigs_info" label="${tool.name}: on ${on_string}: Contigs Info" />
        <data format="tabular" name="alleles" label="${tool.name}: on ${on_string}: Alleles"  />
        <data format="txt" name="log" label="${tool.name}: on ${on_string}: Log" />
        <data format="tabular" name="repeated_loci" label="${tool.name}: on ${on_string}: Repeated Loci" />
    </outputs>
    <tests>
        
    </tests>
    <help><![CDATA[
    ]]>
    </help>
    <citations>
        <citation type="bibtex">
            @ARTICLE{andrews_s,
                author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN
                          and Machado, MP and Oleastro, M and Borges, V and Isidro, J
                          and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK
                          and Halkilahti, J and Jaakkonen, A and Palma, F and Culebro, A
                          and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R
                          and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M
                          and Garaizer, J and Bikandi, J and Hilbert, F and Taboada, EN
                          and Carriço, JA},
                keywords = {bioinformatics, ngs, mlst},
                title = {{INNUENDO whole and core genome MLST databases and schemas
                          for foodborne pathogens}},
                url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}
            }
        </citation>
      <citation type="doi">10.1099/mgen.0.000166</citation>
      <citation type="doi">10.1371/journal.pgen.1007261</citation>
    </citations>
</tool>